Zebrafish: 3D Traction Force Microscopy

Nature Cell Biology, 2022.

This repository contains a sample implementation of our algorithm to compute traction stresses. Please refer to the technical supplemental material for the detailed description and pseudo-code of our algorithm.

Installing

mkdir build
cd build
cmake ..
make -j

The executables under the resources folder are compiled with Clang12 under MacOS High Sierra and Ubuntu 2004.

Dependencies

This implementation mainly relies on the following code bases or tools. CMake should automatically download all external dependencies.

• CLI11: IO support
• Libigl, Eigen: basic routines
• TinyTIFF: TIFF image format support
• Hypre: linear system solver
• LBFGS++: optimization implementation
• tbb: cross-platform parallel computing support

Repository structure

The Cpp folder contains the implementation of our algorithm and the corresponding user interface design:

• gui: contains the design of the GUI interface.
• test: contains the tests and experiments during development. Some functions are out of date.
• main_gui.cpp: the entry point of the GUI.

The MatlabScripts folder contains the development and test code in MATLAB.

The Analysis folder contains the post-analysis code. It takes the displacement as input and computes the desired forces or stresses.

The tests folder contains the unit test of essential components.